2 Answers
2

There may well be a better way, but you can convince OSX to make the change by first renaming it to something without an extension (myProject.xcodeproj becomes myProject), then renaming again, adding the extension back in (myProject becomes myProject.xcodeproj).

Because HFS filesystems hold a lot more metadata than most others, including FAT and NTFS, copying entire branches, e.g. folders of files, onto other filesystems tends to lose stuff like the bundle state.
Different copy methods also have different copy results, depending on whether the invisible files are picked up by the copy.
The best way to address this is by either compressing the whole branch before moving it off HFS, or by keeping the branch on a virtual disk that you mount from your mac as needed.